[gmx-users] Atomtype P,SI not found from grompp

[Jennifer Vo]

Dear Justin,
Thanks again! I have downloaded the topology from Automated Topology
Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using the
existing molecules.

Checking all of the *.itp file with both  GROMOS 54A7  and GROMOS 534A6
force field for all of the NADPH they provided, I see all of these have the
"P,SI" type.
I would like to ask for your advice in this case.
Regards,
Jennifer

On Thu, Jan 15, 2015 at 7:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/15 1:31 PM, Jennifer Vo wrote:
>
>> Dear Justin,
>> Thanks a lot, now I got it. I thought P and SI is the two separated atoms
>> so I searched for them two times. Now the
>> grep "P,SI" *.*
>> returned
>> nap_allatom.itp:    3  P,SI    1    NAP    P2B    1    2.247  30.9738
>> nap_allatom.itp:   21  P,SI    1    NAP     PA    4    2.315  30.9738
>> nap_allatom.itp:   26  P,SI    1    NAP     PN    5    2.259  30.9738
>>
>> should I change "P,SI" to P only?
>>
>
> If the atom name is an indicator of what the atom is, then presumably
> yes.  But I would be wary of any topology in general that used nonsense
> atom types in the parameters it produces, unless there is some additional
> (external) set of parameters upon which this molecule relies, e.g.
> something that defines new parameters and interactions for something called
> "P,SI."
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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